Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate CA265_RS17585 CA265_RS17585 acetyl-CoA acetyltransferase
Query= BRENDA::P45359 (392 letters) >FitnessBrowser__Pedo557:CA265_RS17585 Length = 391 Score = 288 bits (736), Expect = 2e-82 Identities = 167/400 (41%), Positives = 247/400 (61%), Gaps = 24/400 (6%) Query: 3 EVVIASAVRTAIGSYGKSL-KDVPAVDLGATAIKEAVKKA-GIKPEDVNEVILGNVL-QA 59 E I + RTA+G + + + A DL A I+ V + E +++VI+GN +A Sbjct: 2 EAYIIAGYRTAVGKAPRGVFRFTRADDLAAEVIRALVASVPNLDNEQIDDVIVGNATPEA 61 Query: 60 GLGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMS 119 G N R S ++P +T+N+ C SGL T++ A IKAG AD IIAGG+E MS Sbjct: 62 EQGLNIGRMISLMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVMS 121 Query: 120 RAPYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFA 179 P+ G+++ V + D W MG+TAE +A+ +N+SRE+QD F+ Sbjct: 122 GMPF------GGWKLVPNAEVAKNNPDWYWG------MGLTAEAVAKEYNVSREDQDAFS 169 Query: 180 LASQKKAEEAIKSGQFKDEIVPVVI---------KGRKGETVVDTDEHPRFGSTIEGLAK 230 L S +KA AIK+G KD I+P+ + K + VVDTDE PR +T++ LAK Sbjct: 170 LKSHEKAIHAIKNGHLKDGILPITVNENYLDANLKKKTRSYVVDTDEGPRADTTLDKLAK 229 Query: 231 LKPAFKKDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGY 290 LKP F G+VTAGN+S +D AA ++++S +K KEL +P+A++VSYG AGV P IMG Sbjct: 230 LKPVFDAVGSVTAGNSSQTSDGAAFVLVVSEKKMKELNAEPIARLVSYGIAGVPPRIMGI 289 Query: 291 GPFYATKAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPI 350 GP A A+++AG +++DLIE NEAFA+QSLAV + L + + +NVNGGAIALGHP+ Sbjct: 290 GPIEAIPKALKQAGLKKEDIDLIELNEAFASQSLAVIRTLDLNPDVINVNGGAIALGHPL 349 Query: 351 GASGARILVTLVHAMQKRDAKKGLATLCIGGGQGTAILLE 390 G +GA++ V +++ +++++ K G+ T+C+G GQG A + E Sbjct: 350 GCTGAKLTVQIMNELKRQNKKYGMVTMCVGTGQGAAGIFE 389 Lambda K H 0.315 0.132 0.375 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 427 Number of extensions: 21 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 392 Length of database: 391 Length adjustment: 31 Effective length of query: 361 Effective length of database: 360 Effective search space: 129960 Effective search space used: 129960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory